I got a theory, personally call it GAME FUNCTION.
We could divide a game's all mechanics into 3 parts: input, tanslater, output.
All thing players have done are inputs, then the mechanics trans them in to statics, and make some ingame changes based on those translated statics.
All complains about EU4's lack of depth then are also divided into 3 parts, lack of input depth, lack of translater depth and lack of output depth.
1.People complain about beeing limited to do something: can't change government type freely, can't research techs freely but in line, can't do this or that, is of the first type, I mean lack of input depth. People feel that what they can do is limited and no many choices avaliable.
2.People complain about "click A or B to add flag to province/Country X" is of the second type. IMO this part is where the most serious problems are resualted from. Even we can do many things in EU4, and we could change everything, EU4 is still a bland game, because all our operation and all ingame statics are translated so directly and simply. Religions = some statics modifier, so as government type, so as tech group, so as culture, so as almost everything. Comparing with CK2's dynasty management and VIC2's POP, it needs no skill at all. We may not know what a law-change descision will bring to our nation, but we will definitely know that in EU4. All we could do in EU4 is like a maths game, and even maths game of junior middle school level. We do many things, but except conquering, they are just doing some sum or muti operation.
3. Output is also the problem. The only thing important is conquering, and everything is for conquering. We make alliances, managed to westernize, built buildings, just for improve some statics, and all these statatics are leading to more efficient conquering. Nothing more. Could you gain victory in any other way?
This is a small summary to my theory. I wish others and PI could listen to me but I don't care if they don't.